Actually. Pichu is considered stronger than Pikachu by many, as well as Young Link compared to Link. Dr. Mario, someone who spends all day in his lab, has next to no physical exercise (as per trophy) yet he's infinitely more powerful. Zero Suit Samus is already described as faster, and her whip attacks have greater melee range. There are already advantages and we haven't seen her in full. I'd love to be able to use Samus' stunner in the power suit as a setup, but the game didn't allow for that.
I mean, if you wanted Samus but got changed to another character you didn't want to play, wouldn't that be enough of a downside despite how good or bad she is? For a random example, what if using let's say, Wario's Final Smash turned you into Donkey Kong? (makes no sense, just an example.) You wouldn't want that since it's a completely different character from the one you picked. They could have done it simply because it's an option and a way to make it different from the 35+ Final Smashes they have.My post wasn't in disagreement with yours. If anything, supporting it.